AMBER Archive (2005)

Subject: Re: AMBER: gaff frcmod file for TI calculation

From: David A. Case (case_at_scripps.edu)
Date: Wed Feb 02 2005 - 18:44:13 CST

On Wed, Feb 02, 2005, Eric Hu wrote:

> Hi, I used antechamber to generate the frcmod file for
> a small organic molecule. And it turns out the frcmod
> file is empty. I then defined the dummy atom types in
> the pert.frcmod file according to the atom types
> generated by gaff. Now leap complains about all the
> parameters (such as bond, angel and etc), which is
> understandable. However is there a way to make the
> pert.frcmod file without going to gaff.dat and
> redefining all the missing parameters? Thanks.

No, you have to do this by hand. There is no unique (or even "best") way
to make dummy types, so it is hard to see how a program could really do this
anyway.

The perturbation stuff is quite flexible, but admittedly can be tedious to
use.

...dac

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